12 left in tourney - top 5 pay.
6 Handed Table - Avg stack 3k, I have 5K (2nd stack)

One off the button, no action to me; Blinds 50-100.
Im dealt JJ, raise to 300.
Everyone folds to BB who goes all in for 1500.
- I get a read, he is not strong; maybe small pair or at worst AK. I do not believe for a second AA -QQ. I even tell him what I have and am assured that Im good.

So - do you call?
(BTW the read was right - A7 off)

If you read your opponent as weak then why wouldn't you call? I think in your situation with your read it is an easy call. Note that in most tourneys it against the rules to expose your hand (verbally or visually). Be careful because your hand could be ruled dead.

9 at table - blinds 100-200 25 ante. Avg table stack 2500, me at 10K
10 get the $$, 30 left
Im in the BB, everyone folds to short stack on the button goes all in for 1500.
Small blind folds, I look down to 99. I really have no read on the player but am pretty sure he has legetimate hand as he has been tight.

Do you defend?

Again trust your reads. Your stack is too vulnerable to defend "ALL IN" with a coin flip or worse and against an overpair.

I hate min raises. What do they accomplish? Where are you in this hand? How can you be sure? I would be tempted to fold to the raise and reraise. Looks like two players looking for action with big hands. I think at least one has an over pair and at best your probably against a coinflip against the other. Not to sure what buy-in or level you and your opponents are playing but min raise is used by weak players or players trying to trap with their Aces and Kings. If you want to play your 1010 then raise enough to define your hand.

7 Left in Tourney - top 5 pay.
Im in for 3000k with two others who have 6000K.
100-200, Im in small blind, called to see a flop with AQ off against two others.
Flop comes T-8-2 rainbow. Check, check, Last to act raised 2500, I'm sure that this is a semi bluff with maybe 8 or 2.

So- Do you go all in?
(BTW he did have small pair)

Not unless you think your opponent will fold the small pair. I fold and cut my losses here. You have nothing invested seems easy to get away from.

These are the plays that I find are killing me or making me; I am getting to big stack and am calling coin flips, or 2-1 or very rarely worse long shots, with the idea that if I break someone Im one step closer and if I lose I have a stack cushion.

Is this a HUGE hole in my game? Or are these shots that you have to take to win? perhaps I have been watching Moneymaker and Raymer too much?

Seems like your pushing a little harder than you need to. Trust your reads but realize that it is not your duty with a big stack to bust the entire table.

You must also compare your stack to the blinds when comparing your stack to the others in the tourney. When your under 20 BB total it doesn't take many losses to bring you down to the average stack or bellow. When watching the WSOP and/or WPT many times the chip leaders have 100BB's and have a lot of room for play.